diff --git a/R/Calibration.R b/R/Calibration.R
index a66c78154e42b49ab80a61db832a6327da4dd962..3cce7b368bb73854c59f6a6ab2cd91af40731302 100644
--- a/R/Calibration.R
+++ b/R/Calibration.R
@@ -3,17 +3,15 @@ Calibration <- function(InputsModel,
InputsCrit,
CalibOptions,
FUN_MOD,
- FUN_CRIT, # deprecated
FUN_CALIB = Calibration_Michel,
FUN_TRANSFO = NULL,
verbose = TRUE,
...) {
FUN_MOD <- match.fun(FUN_MOD)
- if (!missing(FUN_CRIT)) {
- FUN_CRIT <- match.fun(FUN_CRIT)
- }
+
FUN_CALIB <- match.fun(FUN_CALIB)
+
if (!is.null(FUN_TRANSFO)) {
FUN_TRANSFO <- match.fun(FUN_TRANSFO)
}
diff --git a/R/Calibration_Michel.R b/R/Calibration_Michel.R
index 462cd26185a8d7b89f69269b36e8a40389d0359e..854ab723146e860f20b7e884b7523b68a570cd05 100644
--- a/R/Calibration_Michel.R
+++ b/R/Calibration_Michel.R
@@ -3,16 +3,12 @@ Calibration_Michel <- function(InputsModel,
InputsCrit,
CalibOptions,
FUN_MOD,
- FUN_CRIT, # deprecated
FUN_TRANSFO = NULL,
verbose = TRUE,
...) {
FUN_MOD <- match.fun(FUN_MOD)
- if (!missing(FUN_CRIT)) {
- FUN_CRIT <- match.fun(FUN_CRIT)
- }
# Handling 'FUN_TRANSFO' from direct argument or provided by 'CaliOptions'
if (!is.null(FUN_TRANSFO)) {
@@ -56,9 +52,6 @@ Calibration_Michel <- function(InputsModel,
if (!inherits(CalibOptions, "HBAN")) {
stop("'CalibOptions' must be of class 'HBAN' if 'Calibration_Michel' is used")
}
- if (!missing(FUN_CRIT)) {
- warning("argument 'FUN_CRIT' is deprecated. The error criterion function is now automatically get from the 'InputsCrit' object")
- }
##_variables_initialisation
ParamFinalR <- NULL
diff --git a/R/CreateInputsCrit.R b/R/CreateInputsCrit.R
index 049e89a037ab60bcec6fc11b082bd324459e8143..04e02e7386b93903e0257a804c5c88b9ce7f319a 100644
--- a/R/CreateInputsCrit.R
+++ b/R/CreateInputsCrit.R
@@ -1,16 +1,13 @@
CreateInputsCrit <- function(FUN_CRIT,
InputsModel,
RunOptions,
- Qobs, # deprecated
Obs,
VarObs = "Q",
BoolCrit = NULL,
transfo = "",
Weights = NULL,
- Ind_zeroes = NULL, # deprecated
epsilon = NULL,
- warnings = TRUE,
- verbose = TRUE) { # deprecated
+ warnings = TRUE) {
ObjectClass <- NULL
@@ -18,25 +15,6 @@ CreateInputsCrit <- function(FUN_CRIT,
## ---------- check arguments
- if (!missing(Qobs)) {
- if (missing(Obs)) {
- if (warnings) {
- warning("argument 'Qobs' is deprecated. Please use 'Obs' and 'VarObs' instead")
- }
- Obs <- Qobs
- # VarObs <- "Qobs"
- } else {
- warning("argument 'Qobs' is deprecated. The values set in 'Obs' will be used instead")
- }
- }
- if (!missing(Ind_zeroes) & warnings) {
- warning("deprecated 'Ind_zeroes' argument")
- }
- if (!missing(verbose)) {
- warning("deprecated 'verbose' argument. Use 'warnings', instead")
- }
-
-
## check 'InputsModel'
if (!inherits(InputsModel, "InputsModel")) {
stop("'InputsModel' must be of class 'InputsModel'")
diff --git a/R/ErrorCrit.R b/R/ErrorCrit.R
index e6ef4b4ef3f858c286e68cb680fb23ac191646fb..291337d967744bc7ec2dc3b2fee177a48a92478a 100644
--- a/R/ErrorCrit.R
+++ b/R/ErrorCrit.R
@@ -1,4 +1,4 @@
-ErrorCrit <- function(InputsCrit, OutputsModel, FUN_CRIT, warnings = TRUE, verbose = TRUE) {
+ErrorCrit <- function(InputsCrit, OutputsModel, warnings = TRUE, verbose = TRUE) {
## ---------- Arguments check
@@ -9,10 +9,6 @@ ErrorCrit <- function(InputsCrit, OutputsModel, FUN_CRIT, warnings = TRUE, verbo
if (!inherits(OutputsModel, "OutputsModel")) {
stop("OutputsModel must be of class 'OutputsModel'")
}
- if (!missing(FUN_CRIT)) {
- warning("deprecated 'FUN_CRIT' argument. The error criterion function is now automatically get from the 'InputsCrit' object", call. = FALSE)
- }
-
## ---------- Criterion computation
diff --git a/man/Calibration.Rd b/man/Calibration.Rd
index 7368556f2202b4d24ecfbc9badb85d888fd3fd3c..65d8ee7a3fcd5f91e8d6a57408ae4c2ee285bb85 100644
--- a/man/Calibration.Rd
+++ b/man/Calibration.Rd
@@ -15,7 +15,7 @@ Calibration algorithm that optimises the error criterion selected as objective f
\usage{
Calibration(InputsModel, RunOptions, InputsCrit, CalibOptions,
- FUN_MOD, FUN_CRIT, FUN_CALIB = Calibration_Michel,
+ FUN_MOD, FUN_CALIB = Calibration_Michel,
FUN_TRANSFO = NULL, verbose = TRUE, ...)
}
@@ -31,8 +31,6 @@ Calibration(InputsModel, RunOptions, InputsCrit, CalibOptions,
\item{FUN_MOD}{[function] hydrological model function (e.g. \code{\link{RunModel_GR4J}}, \code{\link{RunModel_CemaNeigeGR4J}})}
-\item{FUN_CRIT}{[function] error criterion function (e.g. \code{\link{ErrorCrit_RMSE}}, \code{\link{ErrorCrit_NSE}})}
-
\item{FUN_CALIB}{(deprecated) [function] calibration algorithm function (e.g. \code{\link{Calibration_Michel}}), \code{default = Calibration_Michel}}
\item{FUN_TRANSFO}{(optional) [function] model parameters transformation function, if the \code{FUN_MOD} used is native in the package \code{FUN_TRANSFO} is automatically defined}
diff --git a/man/Calibration_Michel.Rd b/man/Calibration_Michel.Rd
index 28de8c4424cc84889a83fdbd9a123d5329c7af3f..6befd8b0c9293d84e43fffe5490c594de3ddbd12 100644
--- a/man/Calibration_Michel.Rd
+++ b/man/Calibration_Michel.Rd
@@ -19,7 +19,7 @@ Then a steepest descent local search algorithm is performed, starting from the r
\usage{
Calibration_Michel(InputsModel, RunOptions, InputsCrit, CalibOptions,
- FUN_MOD, FUN_CRIT, FUN_TRANSFO = NULL, verbose = TRUE, ...)
+ FUN_MOD, FUN_TRANSFO = NULL, verbose = TRUE, ...)
}
@@ -34,8 +34,6 @@ Calibration_Michel(InputsModel, RunOptions, InputsCrit, CalibOptions,
\item{FUN_MOD}{[function] hydrological model function (e.g. \code{\link{RunModel_GR4J}}, \code{\link{RunModel_CemaNeigeGR4J}})}
-\item{FUN_CRIT}{(deprecated) [function] error criterion function (e.g. \code{\link{ErrorCrit_RMSE}}, \code{\link{ErrorCrit_NSE}})}
-
\item{FUN_TRANSFO}{(optional) [function] model parameters transformation function, if the \code{FUN_MOD} used is native in the package \code{FUN_TRANSFO} is automatically defined}
\item{verbose}{(optional) [boolean] boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}}
diff --git a/man/CreateInputsCrit.Rd b/man/CreateInputsCrit.Rd
index eed50f03672fc974f63264c022db962ef7a30433..8debd8f93f11e75c27e5234d256d1008da987307 100644
--- a/man/CreateInputsCrit.Rd
+++ b/man/CreateInputsCrit.Rd
@@ -9,16 +9,16 @@
\description{
-Creation of the \code{InputsCrit} object required to the \code{ErrorCrit_*} functions. This function is used to define whether the user wants to calculate a single criterion, multiple criteria in the same time, or a composite criterion, which averages several criteria.
+Creation of the \code{InputsCrit} object required to the \code{ErrorCrit_*} functions. This function is used to define whether the user wants to calculate a single criterion, multiple criteria in the same time, or a composite criterion, which averages several criteria.
}
\usage{
CreateInputsCrit(FUN_CRIT, InputsModel, RunOptions,
- Qobs, Obs, VarObs = "Q", BoolCrit = NULL,
+ Obs, VarObs = "Q", BoolCrit = NULL,
transfo = "", Weights = NULL,
- Ind_zeroes = NULL, epsilon = NULL,
- warnings = TRUE, verbose = TRUE)
+ epsilon = NULL,
+ warnings = TRUE)
}
@@ -29,8 +29,6 @@ CreateInputsCrit(FUN_CRIT, InputsModel, RunOptions,
\item{RunOptions}{[object of class \emph{RunOptions}] see \code{\link{CreateRunOptions}} for details}
-\item{Qobs}{(deprecated) [numeric (atomic or list)] series of observed discharges [mm/time step]}
-
\item{Obs}{[numeric (atomic or list)] series of observed variable ([mm/time step] for discharge or SWE, [-] for SCA)}
\item{VarObs}{(optional) [character (atomic or list)] names of the observed variable (\code{"Q"} by default, or one of \code{"SCA"}, \code{"SWE"}])}
@@ -41,13 +39,9 @@ CreateInputsCrit(FUN_CRIT, InputsModel, RunOptions,
\item{Weights}{(optional) [numeric (atomic or list)] vector of weights necessary to calculate a composite criterion (the same length as \code{FUN_CRIT}) giving the weights to use for elements of \code{FUN_CRIT} [-]. See details}
-\item{Ind_zeroes}{(deprecated) [numeric] indices of the time steps where zeroes are observed}
-
\item{epsilon}{(optional) [numeric (atomic or list)] small value to add to all observations and simulations when \code{"log"} or \code{"inv"} transformations are used [same unit as \code{Obs}]. See details}
\item{warnings}{(optional) [boolean] boolean indicating if the warning messages are shown, default = \code{TRUE}}
-
-\item{verbose}{(deprecated) [boolean] boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}}
}
@@ -62,9 +56,9 @@ CreateInputsCrit(FUN_CRIT, InputsModel, RunOptions,
\emph{$epsilon } \tab [numeric] small value to add to all observations and simulations when \code{"log"} or \code{"inv"} transformations are used [same unit as \code{Obs}] \cr
\emph{$Weights } \tab [numeric] vector (same length as \code{VarObs}) giving the weights to use for elements of \code{FUN_CRIT} [-] \cr
}
-
+
When \code{Weights = NULL}, \code{CreateInputsCrit} returns an object of class \emph{Single} that is a list such as the one described above. \cr
-When \code{Weights} contains at least one \code{NULL} value and \code{Obs} contains a list of observations, \code{CreateInputsCrit} returns an object of class \emph{Multi} that is a list of lists such as the one described above. The \code{\link{ErrorCrit}} function will then compute the different criteria prepared by \code{CreateInputsCrit}. \cr
+When \code{Weights} contains at least one \code{NULL} value and \code{Obs} contains a list of observations, \code{CreateInputsCrit} returns an object of class \emph{Multi} that is a list of lists such as the one described above. The \code{\link{ErrorCrit}} function will then compute the different criteria prepared by \code{CreateInputsCrit}. \cr
When \code{Weights} is a list of at least 2 numerical values, \code{CreateInputsCrit} returns an object of class \emph{Compo} that is a list of lists such as the one described above. This object will be useful to compute composite criterion with the \code{\link{ErrorCrit}} function. \cr
To calculate composite or multiple criteria, it is necessary to use the \code{ErrorCrit} function. The other \code{ErrorCrit_*} functions (e.g. \code{\link{ErrorCrit_RMSE}}, \code{\link{ErrorCrit_NSE}}) can only use objects of class \emph{Single} (and not \emph{Multi} or \emph{Compo}). \cr
}
@@ -84,7 +78,7 @@ Transformations are simple functions applied to the observed and simulated varia
\item \code{""}: no transformation is used (default case)
\item \code{"sqrt"}: squared root transformation
\item \code{"log"}: logarithmic transformation (see below regarding the specific case of KGE or KGE2)
- \item \code{"inv"}: inverse transformation
+ \item \code{"inv"}: inverse transformation
\item \code{"sort"}: sort transformation (the simulated and observed variables are sorted from lowest to highest)
\item \code{"boxcox"}: Box-Cox transformation (see below for details)
\item numeric: power transformation (see below for details)
@@ -114,15 +108,15 @@ library(airGR)
data(L0123001)
## preparation of the InputsModel object
-InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
+InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
Precip = BasinObs$P, PotEvap = BasinObs$E)
## calibration period selection
-Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
## preparation of RunOptions object
-RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J, InputsModel = InputsModel,
+RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J, InputsModel = InputsModel,
IndPeriod_Run = Ind_Run)
## simulation
@@ -144,7 +138,7 @@ InputsCritMulti <- CreateInputsCrit(FUN_CRIT = list(ErrorCrit_RMSE, ErrorCrit_NS
Obs = list(BasinObs$Qmm[Ind_Run], BasinObs$Qmm[Ind_Run]),
VarObs = list("Q", "Q"), transfo = list("", "sqrt"),
Weights = NULL)
-str(InputsCritMulti)
+str(InputsCritMulti)
invisible(ErrorCrit(InputsCrit = InputsCritMulti, OutputsModel = OutputsModel))
## efficiency composite criterion: Nash-Sutcliffe Efficiency mixing
@@ -154,7 +148,7 @@ InputsCritCompo <- CreateInputsCrit(FUN_CRIT = list(ErrorCrit_NSE, ErrorCrit_NSE
Obs = list(BasinObs$Qmm[Ind_Run], BasinObs$Qmm[Ind_Run]),
VarObs = list("Q", "Q"), transfo = list("", "log"),
Weights = list(0.4, 0.6))
-str(InputsCritCompo)
+str(InputsCritCompo)
invisible(ErrorCrit(InputsCrit = InputsCritCompo, OutputsModel = OutputsModel))
}
@@ -165,12 +159,12 @@ Olivier Delaigue, Laurent Coron, Guillaume Thirel
\references{
-Pushpalatha, R., Perrin, C., Le Moine, N. and Andréassian, V. (2012).
- A review of efficiency criteria suitable for evaluating low-flow simulations.
+Pushpalatha, R., Perrin, C., Le Moine, N. and Andréassian, V. (2012).
+ A review of efficiency criteria suitable for evaluating low-flow simulations.
Journal of Hydrology, 420-421, 171-182, doi: 10.1016/j.jhydrol.2011.11.055.
\cr\cr
-Santos, L., Thirel, G. and Perrin, C. (2018).
- Technical note: Pitfalls in using log-transformed flows within the KGE criterion.
+Santos, L., Thirel, G. and Perrin, C. (2018).
+ Technical note: Pitfalls in using log-transformed flows within the KGE criterion.
Hydrol. Earth Syst. Sci., 22, 4583-4591, doi: 10.5194/hess-22-4583-2018.
}
diff --git a/man/ErrorCrit.Rd b/man/ErrorCrit.Rd
index acb933c6b935ddb68b5ebdc23f6cbe7a736bf42c..f183997c7672c0e30692639d9a51903d03d58ef6 100644
--- a/man/ErrorCrit.Rd
+++ b/man/ErrorCrit.Rd
@@ -14,7 +14,7 @@ Function which computes an error criterion with the provided function.
\usage{
-ErrorCrit(InputsCrit, OutputsModel, FUN_CRIT, warnings = TRUE, verbose = TRUE)
+ErrorCrit(InputsCrit, OutputsModel, warnings = TRUE, verbose = TRUE)
}
@@ -23,8 +23,6 @@ ErrorCrit(InputsCrit, OutputsModel, FUN_CRIT, warnings = TRUE, verbose = TRUE)
\item{OutputsModel}{[object of class \emph{OutputsModel}] see \code{\link{RunModel_GR4J}} or \code{\link{RunModel_CemaNeigeGR4J}} for details}
-\item{FUN_CRIT}{(deprecated) [function] error criterion function (e.g. \code{\link{ErrorCrit_RMSE}}, \code{\link{ErrorCrit_NSE}})}
-
\item{warnings}{(optional) [boolean] boolean indicating if the warning messages are shown, default = \code{TRUE}}
\item{verbose}{(optional) [boolean] boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}}
@@ -64,15 +62,15 @@ library(airGR)
data(L0123001)
## preparation of the InputsModel object
-InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
+InputsModel <- CreateInputsModel(FUN_MOD = RunModel_GR4J, DatesR = BasinObs$DatesR,
Precip = BasinObs$P, PotEvap = BasinObs$E)
## calibration period selection
-Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
+Ind_Run <- seq(which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1990-01-01"),
which(format(BasinObs$DatesR, format = "\%Y-\%m-\%d")=="1999-12-31"))
## preparation of RunOptions object
-RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J, InputsModel = InputsModel,
+RunOptions <- CreateRunOptions(FUN_MOD = RunModel_GR4J, InputsModel = InputsModel,
IndPeriod_Run = Ind_Run)
## simulation
@@ -85,7 +83,7 @@ InputsCritSingle <- CreateInputsCrit(FUN_CRIT = ErrorCrit_NSE,
InputsModel = InputsModel, RunOptions = RunOptions,
Obs = list(BasinObs$Qmm[Ind_Run]),
VarObs = "Q", transfo = "",
- Weights = NULL)
+ Weights = NULL)
str(ErrorCrit(InputsCrit = InputsCritSingle, OutputsModel = OutputsModel))
## 2 efficiency critera: RMSE and the Nash-Sutcliffe Efficiency
@@ -93,7 +91,7 @@ InputsCritMulti <- CreateInputsCrit(FUN_CRIT = list(ErrorCrit_RMSE, ErrorCrit_NS
InputsModel = InputsModel, RunOptions = RunOptions,
Obs = list(BasinObs$Qmm[Ind_Run], BasinObs$Qmm[Ind_Run]),
VarObs = list("Q", "Q"), transfo = list("", "sqrt"),
- Weights = NULL)
+ Weights = NULL)
str(ErrorCrit(InputsCrit = InputsCritMulti, OutputsModel = OutputsModel))
## efficiency composite criterion: Nash-Sutcliffe Efficiency mixing
@@ -102,7 +100,7 @@ InputsCritCompo <- CreateInputsCrit(FUN_CRIT = list(ErrorCrit_NSE, ErrorCrit_NSE
InputsModel = InputsModel, RunOptions = RunOptions,
Obs = list(BasinObs$Qmm[Ind_Run], BasinObs$Qmm[Ind_Run]),
VarObs = list("Q", "Q"), transfo = list("", "log"),
- Weights = list(0.4, 0.6))
+ Weights = list(0.4, 0.6))
str(ErrorCrit(InputsCrit = InputsCritCompo, OutputsModel = OutputsModel))
}